New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_pgi	= 4466372	17 (0.880)	3 (0.160)	3/274	2.5	17.1%	coding (878/948 nt)	treR	trehalose 6‑phosphate‑inducible trehalose regulon transcriptional repressor
	?	NC_000913_3_vch_pgi	= 4466464	13 (0.710)					coding (786/948 nt)	treR	trehalose 6‑phosphate‑inducible trehalose regulon transcriptional repressor
Rejected: Frequency below/above cutoff threshold.

AACGGGAACGTTCCCGAAACGCAGCGAAGATCACAATTTATCGTTCAGGAAACGATCAGGACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCG‑TTGCTCTTGCAGGTATTTACTTGCGCCAAGT  >  NC_000913_3_vch_pgi/4466247‑4466518                                                                                                                              |                                                                                                                                                    aaCGGGAACGTTCCCGAAACGCAGCGAAGATCACAATTTATCGTTCAGGAAACGATCAGGACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCg                                                                                                                              <  1:274190/149‑1 (MQ=255)   cGGGAACGTTCCCGAAACGCAGCGAAGATCACAATTTATCGTTCAGGAAACGATCAGGACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGc                                                                                                                            <  1:4293/149‑1 (MQ=255)       accggtCCCGAAACGCAGCGAAGATCACAATTTATCGTTCAGGAAACGATCAGGACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTaa                                                                                                                        <  1:115336/144‑1 (MQ=255)                   aCGCAGCGAAGATCACAATTTATCGTTCAGGACACGATCAGGACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGTGTACCGTCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACg                                                                                                            <  1:115167/149‑1 (MQ=255)                       aGCGAAGATCACAATTTATCGTTCAGGAAACGATCAGGACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCGTCGGCGTAACCGGGATCTACGGGTa                                                                                                        >  1:7927/1‑149 (MQ=255)                          gAAGATCACAATTTATCGTTCAGGAAACGATCAGGACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGa                                                                                                     <  2:135824/149‑1 (MQ=255)                           aaGATCACAATTTATCGTTCAGGAAACGATCAGGACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCgagcgtcggtaatacgccgttaatgaaattcctccatccggagatcgta                                                                                                    >  1:261320‑M1/1‑100 (MQ=255)                               tCACAATTTATCGTTCAGGAAACGATCAGGACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTcc                                                                                                <  1:289007/149‑1 (MQ=255)                                caccATTTATCGTTCAGGAAACGATCAGGACAGGGCGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCAAGCTTCGGCGTAACCGGGCTCTACGGTCACGATCTCCg                                                                                               >  2:25679/1‑149 (MQ=255)                                               aGGAAACGATCAGGACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGTTCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAAtttga                                                                                >  1:150835/1‑147 (MQ=255)                                                    aCGATCAGGACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAAc                                                                           >  1:213235/1‑149 (MQ=255)                                                              cAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCGTGGCTCTGCGTAACCGGGATCTACGGTTACGCTCTCCGGATGGAGGAATTTCATTAACGGCGTATTAc                                                                 <  1:150335/149‑1 (MQ=255)                                                                        gggATGATGCTTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCCAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTCCGGTTACGATCTCCGGCTGGAGGCATTTCATTAACGGCGTTTTTCCTccgcccgc                                                       >  2:163442/1‑149 (MQ=255)                                                                        gggATGATGATTTGTTGAGGTTCGCTGCGCACGGTTACCTGCGAGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTAATTAGCGGCGTGTTCGCGACGCTCgc                                                       <  1:92580‑M2/149‑3 (MQ=255)                                                                             gatgatTTGTTGCGGTTGGCTACGCCCGGTTACCTGCGCGATCCACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAAACGGGATCTACGGCTCCGATCTCGGGATGGAGGAATTTCAGTACCGGCGCATTTCCGACGCCCgcccgtt                                                  <  2:18533‑M2/149‑8 (MQ=255)                                                                             gatgatTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCgccagtt                                                  <  1:140450‑M2/149‑8 (MQ=255)                                                                               tgatTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGCCGCTCGCCAGTTGc                                                >  1:237623/1‑149 (MQ=255)                                                                                 atTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCgagcgtcggtaatacgccgttaatgaaattcctccatccggagatcgtaaccgtagatcccggttacgccgaagctggacgccaggcggcttgccagttgatc                                              <  2:261320‑M1/149‑104 (MQ=255)                                                                                      ttgCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGAATTACCGACGCTCgccagttgaaaggggt                                         <  1:176834‑M2/149‑17 (MQ=255)                                                                                       tgCGGTTCGCGGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTc                                        <  1:63946/149‑1 (MQ=255)                                                                                                               tGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCG‑TTGCTCTTGCGGGTCttt               >  2:217358/1‑149 (MQ=255)                                                                                                               acccctttcaactggCgagcgtcggtaattcgccgttaatgaaattcctccatccggagatcgtaaccgtagatcccggttacgccgaagctggacgccaggcggcttgccagttgatcgcgcaggtaaccgggcgcagcgaaccgcaa                <  1:176834‑M1/142‑134 (MQ=255)                                                                                                                   cgATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCACGGTGTCGATGCG‑TTGATCTTGCAGGTATTTACtt           >  1:71969/1‑149 (MQ=255)                                                                                                                    gATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCgccagttgatcgcgcaggtaaccgggcgcagcgaaccgcaacaaat           <  2:261320‑M2/149‑47 (MQ=255)                                                                                                                      tCAACTCGCAAGCCGCCTGGCGTCCAGCTGACTCGTAACCGGGATCTCCGTTTACGATCACCGGATGGAGGAACGTCAGGATCGGCGTATTGCCGAAGCTAGCCGGTTCGAAGGTGGCCA‑GCGCGTGCTCTTGCCGGTCGTTACtgcct        >  2:39258/1‑145 (MQ=255)                                                                                                                        aaCTGGCgagcgtcggtaatacgccgttaatgaaattcctccatccggagatcgtaaccgtagatcccggttacgccgaagctggacgccaggcggcttgccagttgatcgcgcaggtaaccgggcgcagcgaaccgcaacaaatcatc       <  1:140450‑M1/149‑143 (MQ=255)                                                                                                                        aaCGGGCgggcgtcggaaatgcgccggtactgaaattcctccatcccgagatcggagccgtagatcccgtttacgccgaagctggacgccaggcggcttgccagtggatcgcgcaggtaaccgggcgtagccaaccgcaacaaatcatc       <  2:18533‑M1/149‑143 (MQ=255)                                                                                                                             gCgagcgtcgcgaacacgccgctaattaaattcctccatccggagatcgtaaccgtagatcccggttacgccgaagctggacgccaggcggcttgccagttgatctcgcaggtaaccgtgcgcagcgaacctcaacaaatcatcatccc  <  1:92580‑M1/149‑148 (MQ=255)                                                                                                                              |                                                                                                                                                    AACGGGAACGTTCCCGAAACGCAGCGAAGATCACAATTTATCGTTCAGGAAACGATCAGGACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCG‑TTGCTCTTGCAGGTATTTACTTGCGCCAAGT  >  NC_000913_3_vch_pgi/4466247‑4466518

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.